Unveiling the Pool of Metallophores in Native Environments and Correlation with Their Potential Producers

Abstract

For many organisms, metallophores are essential biogenic ligands that ensure metal scavenging and acquisition from their environment. Their identification is challenging in highly organic matter rich environments like peatlands due to low solubilization and metal scarcity and high matrix complexity. In contrast to common approaches based on sample modification by spiking of metal isotope tags, we have developed a two-dimensional (2D) Solid-phase extraction-Liquid chromatography-mass spectrometry (SPE-LC-MS) approach for the highly sensitive (LOD 40 fmol per g of soil), high-resolution direct detection and identification of metallophores in both their noncomplexed (apo) and metal-complexed forms in native environments. The characterization of peat collected in the Bernadouze (France) peatland resulted in the identification of 53 metallophores by a database mass-based search, 36 among which are bacterial. Furthermore, the detection of the characteristic (natural) metal isotope patterns in MS resulted in the detection of both Fe and Cu potential complexes. A taxonomic-based inference method was implemented based on literature and public database (antiSMASH database version 3.0) searches, enabling to associate over 40% of the identified bacterial metallophores with potential producers. In some cases, low completeness with the MIBiG reference BCG might be indicative of alternative producers in the ecosystem. Thus, coupling of metallophore detection and producers’ inference could pave a new way to investigate poorly documented environment searching for new metallophores and their producers yet unknown.

A Practical Toolkit for the Detection, Isolation, Quantification, and Characterization of Siderophores and Metallophores in Microorganisms

“…The presence of a putative BGC not only provides evidence that a siderophore is being produced but also can be used to predict the chemical structure of the molecule and dereplicate it against known compounds. Several platforms have been developed for the automated detection of BGCs in a genome, and two of the most popular are antiSMASH and PRISM. , AntiSMASH is a rapid and reliable source for finding gene clusters responsible for the biosynthesis of secondary metabolites and has been widely applied to the discovery of new and known siderophores. − The antiSMASH analysis pipeline, designed for bacterial genomes, and its recent counterpart, fungiSMASH for fungal genomes, share a common codebase. Both pipelines offer specific options through their respective web submission forms.…”

“… 121 , 122 AntiSMASH is a rapid and reliable source for finding gene clusters responsible for the biosynthesis of secondary metabolites and has been widely applied to the discovery of new and known siderophores. 123 − 125 The antiSMASH analysis pipeline, designed for bacterial genomes, and its recent counterpart, fungiSMASH for fungal genomes, share a common codebase. Both pipelines offer specific options through their respective web submission forms.…”